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There is a fee schedule for the USPTO's services. There are fees to file a PPA and more expensive fees for an NPA. Generally, fees are lower for smaller entities. There is a micro-entity fee and a small entity fee for most fee items. There are fees related to appeals, to requesting an IPR, and to a reissue application.

Generally fees are due at filing although, depending upon the fee, they can be delayed for an additional surcharge.

There is a process called reissue that allows the patent owner to declare that their granted patent is deficient in some way and get a re-examination, often involving amending the claims. You can't expand beyond the original disclosure and the defect can be "I didn't claim as broadly as I could have claimed."